feat: minor update

nahid18 · Sep 25, 2023 · 8d1a9d4 · 8d1a9d4
1 parent 395f5ee
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Showing 5 changed files with 13 additions and 11 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: easylift
 Title: An R package to perform genomic liftover
-Version: 0.99.4
+Version: 0.99.5
 Date: 2023-09-25
 Authors@R: 
     c(

diff --git a/R/easylift.R b/R/easylift.R
@@ -46,16 +46,18 @@
 #' which is the basis for \code{easylift}.
 #' @export
 easylift <- function(x, to, chain) {
-  # Check if genome(x) has multiple unique values
+  # Check if GRanges object is provided
+  if (anyNA(GenomeInfoDb::genome(x))) {
+    stop("The genome information is missing. Please set genome(x) before using easylift.")
+  }
+
+  # Check if the input GRanges contains genomic coordinates from multiple genomes
   unique_genomes <- unique(GenomeInfoDb::genome(x))
   if (length(unique_genomes) > 1) {
     stop("The 'GRanges' object 'x' contains genomic coordinates from multiple genomes. ",
          "Please provide 'x' with coordinates from a single genome assembly.")
   }
 
-  if (anyNA(GenomeInfoDb::genome(x))) {
-    stop("The genome information is missing. Please set genome(x) before using easylift.")
-  }
   # Convert the input GRanges to the "UCSC" seqlevels style if not already
   if (GenomeInfoDb::seqlevelsStyle(x) != "UCSC") {
     GenomeInfoDb::seqlevelsStyle(x) <- "UCSC"

diff --git a/README.Rmd b/README.Rmd
@@ -71,7 +71,7 @@ easylift(gr, "hg38")
 To cite package ‘easylift’ in publications use:
 
   Al Nahid A, Love M (2023). _easylift: An R package to perform
-  genomic liftover_. R package version 0.99.4,
+  genomic liftover_. R package version 0.99.5,
   <https://github.com/nahid18/easylift>.
 
 
@@ -82,7 +82,7 @@ A BibTeX entry for LaTeX users is
     title = {easylift: An R package to perform genomic liftover},
     author = {Abdullah Al Nahid and Michael Love},
     year = {2023},
-    note = {R package version 0.99.4},
+    note = {R package version 0.99.5},
     url = {https://github.com/nahid18/easylift},
   }
 ```

diff --git a/README.md b/README.md
@@ -69,7 +69,7 @@ easylift(gr, "hg38")
 To cite package ‘easylift’ in publications use:
 
 Al Nahid A, Love M (2023). *easylift: An R package to perform genomic
-liftover*. R package version 0.99.4,
+liftover*. R package version 0.99.5,
 <https://github.com/nahid18/easylift>.
 
 A BibTeX entry for LaTeX users is
@@ -78,7 +78,7 @@ A BibTeX entry for LaTeX users is
         title = {easylift: An R package to perform genomic liftover},
         author = {Abdullah Al Nahid and Michael Love},
         year = {2023},
-        note = {R package version 0.99.4},
+        note = {R package version 0.99.5},
         url = {https://github.com/nahid18/easylift},
       }
 

diff --git a/tests/testthat/test-easylift.R b/tests/testthat/test-easylift.R
@@ -67,9 +67,9 @@ test_that("easylift succeeds with BiocFileCache", {
   expect_true(nrow(q) > 0, "Chain file should exist in cache.")
 
   # Create a test GRanges object
-  gr <- GRanges(
+  gr <- GenomicRanges::GRanges(
     seqname = Rle(c("chr1", "chr2"), c(100000, 100000)),
-    ranges = IRanges(start = 1, end = 200000)
+    ranges = IRanges::IRanges(start = 1, end = 200000)
   )
 
   genome(gr) <- "hg19"